Ok, here's the solution. It is in fact the same as desribed above, with a new file *_loc.rss added to the project and holding the localizable registration resource.
That is then linked to the *_reg.rss as described above.
RESOURCE LOCALISABLE_APP_INFO r_local_qtmwappwithicon
short_caption = "AppIcon";
caption = "App With Icon";
number_of_icons = 1; // each icon must be a bitmap/mask pair
icon_file = "\\resource\\apps\\qtmwappwithicon.mif";
The *.mif file I've used is one built already for the helloworldbasic example, I've just make a copy of it in place (at \epoc32\release\winscw\udeb\z\resource\apps ).
localisable_resource_id = R_LOCAL_QTMWAPPWITHICON;
The additions to the MMP file:
start resource QtMWAppWithIcon_loc.rss
START RESOURCE "QtMWAppWithIcon_reg.rss"
Finally, the new built files should be added to the package (*.pkg), in my case
Remember to set all modified files as read only and as you don't really want to prevent to make legitimate changes to them you will have to apply the hacks only when the project is otherwise completed.